Research workbench
Crystal structure of photinus pyralis luciferase PPS6 mutant in complex with dlsa
Analyse Crystal structure of photinus pyralis luciferase PPS6 mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q2M
- Type
- protein
- Length
- 1,494 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Luciferin 4-monooxygenase
- EC
- 1.13.12.7
- UniProt
- P08659
- Ligands
- DYD, SLU, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 544 | 31% helix, 25% strand | P08659 |
| B | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 512 | 31% helix, 20% strand | P08659 |
| C | Luciferin 4-monooxygenase (EC 1.13.12.7) | protein | 438 | 32% helix, 23% strand | P08659 |
Ligands and binding sites
- DYD · (2S,5S)-hexane-2,5-diol · ligand · 4 copies · chains A, C
- SLU · 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 39 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.85 | 0.87 | 105 | EDO, SLU |
| 2 | 879 | 0.81 | 0.84 | 110 | EDO, SLU |
| 3 | 466 | 0.74 | 0.83 | 75 | DYD, EDO, SLU |
| 4 | 148 | 0.63 | 0.85 | 28 | empty |
| 5 | 193 | 0.61 | 0.83 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 362 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 324 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 185 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6Q2M · Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA · the same entry in another collection · chain A against A, TM-score 1.00
- P08659 · AlphaFold monomer V2.0 prediction for luciferin 4-monooxygenase (P08659) · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P08659
- Elsewhere: RCSB PDB 6Q2M · PDBe 6Q2M · UniProt P08659
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